There usually isn't as much to worry about (as far as metal removal). What Ford did is they turned both sides of the bushing area of the rod. If you inspect a few, you'll see that they removed a little material from certain rods. I don't try to do that as my little lathe doesn't have enough swing for the rod. If I had a bigger lathe, I'd make a fixture plate so I could do it like Ford did.
I just take the ends to a belt sander - and sometimes a bit to the upper beams. As you might know, you have to balance each end of the rod separately. And also get to the final weight being the same.
Hmmmm . . . I guess I could make a fixture plate for my rotary table and do it on a mill? That gives me a new idea! (Like I need any more damn flathead specific projects!). LOL